Map to CCP4 Style Mask
Hi All, Is there a quick and easy way in Chimera to impose a density level cutoff and write out a ccp4 style mask file? Thanks, Martin Martin Lawrence Department of Chemistry and Biochemistry Montana State University Bozeman, MT 59717 USA
Hi Martin, You can set the threshold level with the “volume” command. I’m not familiar with “ccp4 style mask file” (and as far as I know Chimera doesn’t write mask files), but you can do the masking by the isosurface directly in Chimera with the “mask” command. Example: volume #0 level 0.02 mask #0 #0 model #1 That example has the trivial case of masking the volume by its own isosurface, but you can mask a map by the isosurface of some other map (or various surfaces created in different ways). The “volume” and “mask” commands have lots of options, see: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mask.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 20, 2017, at 7:30 AM, Martin Lawrence <lawrence@chemistry.montana.edu> wrote:
Hi All, Is there a quick and easy way in Chimera to impose a density level cutoff and write out a ccp4 style mask file? Thanks, Martin
Hi Martin, The vop threshold Chimera command can set all the map values below a specified density level to 0, and all the values above that level to 1 creating a mask. For example, vop threshold #0 min 6.5 set 0 max 6.5 setmax 1 Then you can save the new map to a file with Volume Viewer menu entry File / Save Map... or command vol #1 save ~/Desktop/mask.mrc Tom
On Oct 20, 2017, at 7:30 AM, Martin Lawrence wrote:
Hi All,
Is there a quick and easy way in Chimera to impose a density level cutoff and write out a ccp4 style mask file?
Thanks, Martin
Martin Lawrence Department of Chemistry and Biochemistry Montana State University Bozeman, MT 59717 USA
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Elaine Meng -
Martin Lawrence -
Tom Goddard